Mark C. Williams, Northeastern University

How Proteins Use Thermodynamics to Fight Over DNA

Optical tweezers allow us to probe the interactions of proteins with single DNA molecules and apply very small forces. Measurement of force-dependent DNA conformations allows us to quantify interactions that govern cellular function. DNA forms a stable double-helix in order to store the genetic information for most organisms. However, in the process of replicating an organism’s genome, the two strands of the helix must be separated to form single-stranded DNA (ssDNA). This intermediate state is vulnerable to interference from many cellular processes and is therefore tightly regulated.

I will discuss how the protein SSB from the model bacterium E. coli uses a complex and dynamic wrapping mechanism to control access to ssDNA during normal replication. I will then describe a protein in human cells (APOBEC3G) that occupies and/or modifies ssDNA that is formed during retroviral replication, helping to confer immunity to HIV under some conditions. APOBEC3G uses multiple biophysical and biochemical mechanisms to inhibit viral replication and induce viral mutations, which we dissect using single molecule methods. The results demonstrate complex biophysical mechanisms that regulate ssDNA access across a range of organisms and cell types.

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